All File Changes

v437_preview to v437_preview2 (2022-09-05 to 2022-09-12) v437

• confs/preview.hg.conf
  • lines changed 2, context: html, text, full: html, text
    3481a3eb873dfb4276dfd1f8cddf2c59cd1f36f8 Sun Sep 11 01:11:22 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/gar/gar.cgi.pl
  • lines changed 11, context: html, text, full: html, text
    353a13754f34e9cb62a9a841ae64e80c64fbe1d8 Fri Sep 9 18:47:21 2022 -0700
    protect against empty spam bot activity no redmine
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 7, context: html, text, full: html, text
    fb0c581ba94fd1ca33d57e3253f732cd4c4ea62a Fri Aug 26 10:51:31 2022 -0700
    Support Auspice JSON output for monkeypox: url settings not just files, Nextclade_lineage, non-hardcoded Auspice config header, correct amino acid changes on - strand genes.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 328, context: html, text, full: html, text
    fb0c581ba94fd1ca33d57e3253f732cd4c4ea62a Fri Aug 26 10:51:31 2022 -0700
    Support Auspice JSON output for monkeypox: url settings not just files, Nextclade_lineage, non-hardcoded Auspice config header, correct amino acid changes on - strand genes.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 18, context: html, text, full: html, text
    1b074613b1c6b7f84953c3f490631b91d844c9a9 Thu Sep 8 22:40:20 2022 -0700
    Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989
• src/hg/hgVai/hgVai.c
  • lines changed 5, context: html, text, full: html, text
    8d6ff9f56618bcc7ddfed8dfb653127f9aec1912 Tue Sep 6 13:11:49 2022 -0700
    Restoring some dyStringPrintfs that were inadvertently changed to sqlDyStringPrintf but are not for sql. refs #29973
• src/hg/hgc/bigDbSnpClick.c
  • lines changed 33, context: html, text, full: html, text
    1b074613b1c6b7f84953c3f490631b91d844c9a9 Thu Sep 8 22:40:20 2022 -0700
    Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989
• src/hg/hgc/hgc.c
  • lines changed 62, context: html, text, full: html, text
    1b074613b1c6b7f84953c3f490631b91d844c9a9 Thu Sep 8 22:40:20 2022 -0700
    Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989
• src/hg/hgc/hgc.h
  • lines changed 11, context: html, text, full: html, text
    1b074613b1c6b7f84953c3f490631b91d844c9a9 Thu Sep 8 22:40:20 2022 -0700
    Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989
• src/hg/htdocs/goldenPath/help/bigRmsk.html
  • lines changed 13, context: html, text, full: html, text
    8eadcb210a91b4c9aefdd603cd91dfea41340f47 Wed Sep 7 12:08:48 2022 -0700
    update bigRmsk doc to point to the new RepeatMasker release
  • lines changed 15, context: html, text, full: html, text
    cd059caf16656b4fba59a5c9b841978293582dab Wed Sep 7 13:51:38 2022 -0700
    Minor edits to page, refs #29356
  • lines changed 27, context: html, text, full: html, text
    8c520f540bf2410ce30bbf71f16f292b90144a5a Wed Sep 7 14:06:50 2022 -0700
    Fixing merge, going with markD's changes refs #29356
  • lines changed 183, context: html, text, full: html, text
    8b8e3dd40b5f555d315dafce8a4bd64ad07bb1b2 Fri Sep 9 12:51:21 2022 -0700
    Proofread and edited for clarity refs #29356
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    8d4a6be8a26a5156c97267e1f624eade31e1b365 Mon Sep 5 17:32:03 2022 -0700
    releasing and announcing education module
• src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html
  • lines changed 39, context: html, text, full: html, text
    8b8e3dd40b5f555d315dafce8a4bd64ad07bb1b2 Fri Sep 9 12:51:21 2022 -0700
    Proofread and edited for clarity refs #29356
• src/hg/htdocs/indexNews.html
  • lines changed 2, context: html, text, full: html, text
    8d4a6be8a26a5156c97267e1f624eade31e1b365 Mon Sep 5 17:32:03 2022 -0700
    releasing and announcing education module
• src/hg/htdocs/training/index.html
  • lines changed 4, context: html, text, full: html, text
    8d4a6be8a26a5156c97267e1f624eade31e1b365 Mon Sep 5 17:32:03 2022 -0700
    releasing and announcing education module
  • lines changed 1, context: html, text, full: html, text
    649c7c5158dafed90c531259103a36ee0a7afd96 Tue Sep 6 14:21:52 2022 -0700
    one-char typo edit
• src/hg/inc/hui.h
  • lines changed 17, context: html, text, full: html, text
    1b074613b1c6b7f84953c3f490631b91d844c9a9 Thu Sep 8 22:40:20 2022 -0700
    Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    806ed36b35f9db392dadd975839426718339304d Fri Sep 2 14:05:50 2022 -0700
    Oops, removing the duplicate declaration for trackHubGetGenomeUndecorated found by Chris in code review. refs #29936
• src/hg/js/subCfg.js
  • lines changed 7, context: html, text, full: html, text
    1b074613b1c6b7f84953c3f490631b91d844c9a9 Thu Sep 8 22:40:20 2022 -0700
    Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    a7532552dd69ca4d3869f5a4314c0fadfa63dabf Fri Sep 9 11:07:05 2022 -0700
    skip hub_ prefix when looking for curated hubs
• src/hg/lib/hui.c
  • lines changed 138, context: html, text, full: html, text
    1b074613b1c6b7f84953c3f490631b91d844c9a9 Thu Sep 8 22:40:20 2022 -0700
    Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989
  • lines changed 1, context: html, text, full: html, text
    db7b434c0784da31fabea8308639ec60a7ca2da8 Thu Sep 8 23:49:37 2022 -0700
    Little fix since more keywords were added to the end of the bigGenePred type. hui.c and fixes for dbSnp153+
• src/hg/makeDb/doc/hg19.txt
  • lines changed 69, context: html, text, full: html, text
    3ec510efd881b049639d056fb2a58c67d9951ccd Wed Sep 7 16:03:29 2022 -0700
    add hg19 HGNC track
• src/hg/makeDb/doc/ortMon1/initialBuild.txt
  • lines changed 1274, context: html, text, full: html, text
    3ec510efd881b049639d056fb2a58c67d9951ccd Wed Sep 7 16:03:29 2022 -0700
    add hg19 HGNC track
• src/hg/makeDb/doc/panPan3/initialBuild.txt
  • lines changed 7, context: html, text, full: html, text
    27d9d88ca49e60586c2d0b211971c8a360d862ac Thu Sep 8 23:00:48 2022 -0700
    sequenceName alias should properly be called assembly no redmine
• src/hg/makeDb/trackDb/TOGAannotation.html
  • lines changed 34, context: html, text, full: html, text
    fe64746a8641a29b07cb641312297726e6ed4468 Wed Sep 7 15:50:58 2022 -0700
    adding description page for TOGA tracks refs #29982
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    11bfdf3690ae4c00c49d96119942865d1632c843 Wed Sep 7 13:09:33 2022 -0700
    Adding extra index to the Illumina 450K/850K tracks, refs #29309
• src/hg/makeDb/trackDb/human/hg38/cons470way.html
  • lines changed 12, context: html, text, full: html, text
    01f7c63de3412c46292af37d9914134077f47cd2 Tue Sep 6 11:32:51 2022 -0700
    name fixups and set default on species refs #29898
• src/hg/makeDb/trackDb/human/hg38/gtexSingleCell.ra
  • lines changed 4, context: html, text, full: html, text
    78c116ab4c7e58b0a5ac9cb4d4344de768bbda05 Fri Sep 9 08:55:43 2022 -0700
    Fix gtex single cell nuclie hive links and incorrect default track visibility, refs #29954
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 2, context: html, text, full: html, text
    01f7c63de3412c46292af37d9914134077f47cd2 Tue Sep 6 11:32:51 2022 -0700
    name fixups and set default on species refs #29898
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    11bfdf3690ae4c00c49d96119942865d1632c843 Wed Sep 7 13:09:33 2022 -0700
    Adding extra index to the Illumina 450K/850K tracks, refs #29309
• src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html
  • lines changed 326, context: html, text, full: html, text
    105f1ebf5354bd63abb130b087eeca6ad7d649cf Thu Sep 8 22:59:48 2022 -0700
    improvements to SGDP track doc
• src/hg/makeDb/trackDb/human/hs1/ncbiRefSeq.trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    f1032f731437a1dbc14a4a2b1be404ec929350ae Fri Sep 9 17:03:13 2022 -0700
    moving the ncbiRefSeq files to /gbdb/hs1/ncbiRefSeq/ refs #29762
• src/hg/makeDb/trackDb/human/hs1/sgdpCopyNumber.trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    47e244609a3be025f2dd3d672fb52df3b6b9c251 Thu Sep 8 19:00:21 2022 -0700
    removed SGDP score filter and added a minimum copy number filter
  • lines changed 2, context: html, text, full: html, text
    2f6224ae696a43682d125109e03b17442363c32a Thu Sep 8 19:27:49 2022 -0700
    improve SGDP filter label
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    1b074613b1c6b7f84953c3f490631b91d844c9a9 Thu Sep 8 22:40:20 2022 -0700
    Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    1b074613b1c6b7f84953c3f490631b91d844c9a9 Thu Sep 8 22:40:20 2022 -0700
    Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 28, context: html, text, full: html, text
    aaced70d252c2ef4bea708a182da0ecb3987a8c1 Wed Sep 7 10:52:40 2022 -0700
    adding TOGA vs. hg38 and vs. galGal6 tracks to database assemblies refs #29982
  • lines changed 2, context: html, text, full: html, text
    fe64746a8641a29b07cb641312297726e6ed4468 Wed Sep 7 15:50:58 2022 -0700
    adding description page for TOGA tracks refs #29982
• src/hg/utils/automation/aliasTextToBed.pl
  • lines changed 1, context: html, text, full: html, text
    7aefb4e6059a96c47f3ab3b89745bf0f1c697fba Thu Sep 8 14:26:08 2022 -0700
    perfectly strict recognizing old style files no redmine
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
  • lines changed 4, context: html, text, full: html, text
    e1df6d7bb91a0f8027129677be73ad720d79449d Fri Aug 26 11:38:42 2022 -0700
    Update nextstrain URL and use curl --compressed (thanks @tsibley).
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 61, context: html, text, full: html, text
    879c1d08bc8edc582bf06681567834590824ad4c Fri Aug 26 11:51:10 2022 -0700
    Update branch length filter, annotated clades & lineages using previous day's paths for speed, add Taxonium v2 output, add MSA of public sequences.
• src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl
  • lines changed 6, context: html, text, full: html, text
    d01d503c098b25411a732c2190fde29911293822 Fri Aug 26 11:51:59 2022 -0700
    Update nextclade column offsets.
• src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
  • lines changed 39, context: html, text, full: html, text
    1af2f775e2a9c148f0cbff583910f1d68faf2598 Fri Aug 26 11:54:35 2022 -0700
    Do a little more cleanup and always construct name from components; fasta names are not always updated
• src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
  • lines changed 3, context: html, text, full: html, text
    fa70926eb39b233849ef2a1f0e36f4ed264dc832 Fri Aug 26 11:55:24 2022 -0700
    Bump up maxMissing, sometimes there are just a ton.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
  • lines changed 29, context: html, text, full: html, text
    e4eb9b464422dc81af82a711fd6470174ed3fb92 Fri Aug 26 11:56:30 2022 -0700
    Add retry for all the URLs. Update to latest nextclade version.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 28, context: html, text, full: html, text
    72afe80e5fc9ade5df012cfb159e39d5ee953d92 Fri Aug 26 11:59:25 2022 -0700
    Add --debug to datasets command to assist in debugging failures. Patch some corrupted associations between nucleotide IDs and BioSample IDs until the fixes percolate through all the databases. Update to latest versions of nextclade and pangolin.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 547, context: html, text, full: html, text
    84e8a21220c712339da59a4c53ed481162c64156 Fri Aug 26 12:00:07 2022 -0700
    Add IDs for a bunch of new recombinants.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
  • lines changed 9, context: html, text, full: html, text
    02e715d7eb789c5a3fc5399dc6138e94f4fdaa85 Fri Aug 26 12:02:40 2022 -0700
    Add a hook for a prevDate.masked.useMe.pb file so I can do some major pruning, and let sequences be added back the next day without worrying that I've removed too much from the version used by hgPhyloPlace. Update column indices for latest version of nextclade.
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
  • lines changed 33, context: html, text, full: html, text
    b798ee59931597499ea8fe9d4b18e7c2ca26b235 Fri Aug 26 12:04:40 2022 -0700
    Many accumulated tweaks, corrections, for ongoing Omicron lineages & sequencing/assembly errors.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
  • lines changed 4, context: html, text, full: html, text
    6cbc26d41876505e15a244a476f70d9314adc08d Fri Aug 26 12:06:28 2022 -0700
    Add latest Nextstrain clades for Omicrons of concern: 22A=BA.4, 22B=BA.5, 22C=BA.2.12.1, 22D=BA.2.75.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 17, context: html, text, full: html, text
    f0ab7f27d98fd3f3f0506a5da4e1f533b827cff4 Fri Aug 26 12:09:20 2022 -0700
    Add some masked sites to BA.2.10.4 path as new sequences make the lineage root wiggle around a bit. Add new lineages BL.1, BA.2.75.3-5, BA.4.8, BA.5.1.12-14, BF.15-16, BA.5.2.6-7, XAS, XAT, XAU, XAV, renaming proposed* lineages that were designated.
• src/hg/utils/otto/sarscov2phylo/pangoHash.sh
  • lines changed 1, context: html, text, full: html, text
    428e9023e880b56314b2a1b9725415f269f1e54a Fri Aug 26 11:42:45 2022 -0700
    Use minimap2 -x asm20 --score-N=0 as pangolin does, to ensure consistent alignment to reference before masking & hashing.
• src/hg/utils/otto/sarscov2phylo/runNextclade.sh
  • lines changed 9, context: html, text, full: html, text
    8a78f2f53d1ee8640a4f326765646466b5dcfa5b Fri Aug 26 11:43:56 2022 -0700
    Updating usage for latest version of nextclade.
• src/hg/utils/otto/sarscov2phylo/runPangolin.sh
  • lines changed 5, context: html, text, full: html, text
    4a51b1bbc3d9b23dd5a36e4712250ec89f009c2c Fri Aug 26 11:44:17 2022 -0700
    Updating usage for pangolin v4.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 55, context: html, text, full: html, text
    1c62f40bec46afc1a9ad8ee35909008c47d57713 Fri Aug 26 12:20:28 2022 -0700
    Use @yceh's usher-sampled and updated matOptimize instead of running usher on the cluster. Prune before optimization in addition to afterwards in order to avoid some weird moves caused by low-quality long-branch sequences. Annotate clades & lineages using previous day's paths for speed. Add Taxonium v2 output.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
  • lines changed 9, context: html, text, full: html, text
    fda84c0982a6c223bde5a3c295890b8ca6189e05 Fri Aug 26 11:45:28 2022 -0700
    When maintaining consistent mappings of duplicated items, make sure the names really match.
• src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
  • lines changed 12, context: html, text, full: html, text
    6e75f968aeec30536982821ebc0779760af6db3d Fri Aug 26 11:47:28 2022 -0700
    Dropped to 28 jobs instead of 32 because we have some dead cluster nodes. This is no longer used -- @yceh's usher-sampled is way faster -- just committing changes for the record.
• src/hg/utils/otto/sarscov2phylo/util.sh
  • lines changed 1, context: html, text, full: html, text
    ee396acb1919923fb78c5b91b6b17789efba3ca3 Fri Aug 26 11:40:49 2022 -0700
    More regex-cleaning of outlandish things that people put in GenBank titles.
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    813fe4b4d5b0b37734743735a0e43fe96d9a5674 Fri Aug 26 11:12:22 2022 -0700
    Add -ldl to L for CONDA_BUILD; not sure why it wasn't necessary ~v417 but was ~v426.
• src/lib/bbiAlias.c
  • lines changed 4, context: html, text, full: html, text
    1eb157e704df43fc4f530be034e7a934475c2b0b Fri Sep 9 11:26:06 2022 -0700
    require at least one extra index of a chromAlias bigBed
• src/oneShot/preProcGgfAndy/makefile
  • lines changed 12, context: html, text, full: html, text
    6701b09b911c195032edf2090f2363fec47b9464 Fri Aug 26 11:16:13 2022 -0700
    Modernize makefile of obscure program than an MLQ user actually wanted to use. refs #29758
• src/product/installer/browserSetup.sh
  • lines changed 4, context: html, text, full: html, text
    3bb84e0c93fe5e39aeb6384d1572afc2433e17bf Tue Sep 6 06:33:32 2022 -0700
    fixing Gbic with certain combinations of mysql versions and underlying linux, refs #29847
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 25, context: html, text, full: html, text
    9b033f6d0e8b14a79908339c61c7153e7004f19b Thu Sep 8 12:27:11 2022 -0700
    change bedToBigBed to actually describe the use of chromAlias
  • lines changed 3, context: html, text, full: html, text
    87c907ef671a3f51d3a5dc361f8b7446499171f4 Fri Sep 9 11:12:34 2022 -0700
    improved wording for of bedToBigBed help per Max's suggestion
• src/utils/bedToBigBed/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    9b033f6d0e8b14a79908339c61c7153e7004f19b Thu Sep 8 12:27:11 2022 -0700
    change bedToBigBed to actually describe the use of chromAlias
• src/utils/qa/hubPublicAutoUpdate
  • lines changed 1, context: html, text, full: html, text
    58335a3163bdc1d004cd90e61124acfff01fc6d0 Tue Sep 6 16:39:56 2022 -0700
    Editing the script to have curl.bad due to /bin/curl getting changed, no RM
• src/utils/qa/hubPublicUrlChanger
  • lines changed 63, context: html, text, full: html, text
    01dcedd72968b8c72288fbd736032ca902bb0426 Wed Sep 7 13:48:54 2022 -0700
    Adding useful script to git, No RM
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    acbf6b4a4c340858275c845ea97e69eca075e7be Mon Sep 12 10:02:01 2022 -0700
    v437 preview2, refs #29979
• src/utils/vcfFilter/vcfFilter.c
  • lines changed 5, context: html, text, full: html, text
    3fe189a61a18660027dddf81d724f95fd09b56c3 Fri Aug 26 11:14:37 2022 -0700
    Fix bug in dynamic resizing (forgot to update db->size); required to support larger-than-SARS* genomes like monkeypox.

• lines changed: 3739
• files changed: 72